Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_00465 (263 letters) >FitnessBrowser__Caulo:CCNA_02751 Length = 332 Score = 171 bits (432), Expect = 2e-47 Identities = 101/250 (40%), Positives = 144/250 (57%), Gaps = 13/250 (5%) Query: 13 LLDIRGLRKQY--GPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQI 70 ++ + + K Y G L GV LS++ G V +IG+SG+GK+TL+R +N LE GQ+ Sbjct: 1 MITFQDVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQV 60 Query: 71 VLDGESIGYDDIDGKRVRHPEKLIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKL 130 ++DG+ + + G R R GM FQ FNL T QNV L K+ Sbjct: 61 IVDGDDVAALGVAGLRAL---------RRRVGMIFQHFNLLSGKTVAQNVAFPL-KLAGR 110 Query: 131 PKDEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALD 190 P E A + LERVGL +P QLSGGQ+QRV IARA+A NP ++L DE TSALD Sbjct: 111 PAAEVKARTAELLERVGLSAHAGKYPAQLSGGQKQRVGIARALATNPKVLLCDEATSALD 170 Query: 191 PELVGEVLNVIKGL-AEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFERP 249 PE ++L++I GL E G+T++L+THEM V D++ ++ GR+ E+G +E+F P Sbjct: 171 PETTEQILDLIAGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEVFLHP 230 Query: 250 QSPRLAEFLK 259 S F++ Sbjct: 231 ASDTARRFVR 240 Lambda K H 0.320 0.138 0.392 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 208 Number of extensions: 11 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 263 Length of database: 332 Length adjustment: 26 Effective length of query: 237 Effective length of database: 306 Effective search space: 72522 Effective search space used: 72522 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory